gn: Delete genenetwork3 package

* gn/packages/genenetwork.scm (genenetwork3): Delete it. The python3 version
of genenetwork2 is already packaged as python3-genenetwork2.

1 files changed, 0 insertions, 132 deletions

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 7946f70..6641ae6 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -591,138 +591,6 @@ Graphical Fragment Assembly} files and related formats.")
 written in C")
      (license license:agpl3+))))
 
-(define-public genenetwork3
-  (let (;; (commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")
-        (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9"))
-    (package
-     (name "genenetwork3")
-     (version (string-append "2.10rc5-" (string-take commit 7) ))
-     (source (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/fredmanglis/genenetwork2.git")
-               ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
-               ;; (url "https://github.com/genenetwork/genenetwork2_diet.git")
-               (commit commit)))
-        (file-name (string-append name "-" version))
-        (sha256
-         (base32
-          "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di"
-          ;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"
-          ))))
-     (propagated-inputs ;; propagated for development purposes
-      `(;; Agnostic to Python
-        ("r" ,r)
-        ("git" ,git)
-        ("vim" ,vim)
-        ("grep" ,grep)
-        ("which" ,which)
-        ("r-ctl" ,r-ctl)
-        ("r-qtl" ,r-qtl)
-        ("redis" ,redis)
-        ("mariadb" ,mariadb)
-        ("nginx" ,nginx)
-        ("r-wgcna" ,r-wgcna)
-        ;; ("r-phewas" ,r-phewas)
-        ("coreutils" ,coreutils)
-        ("gemma" ,gemma-gn2-git)
-        ("plink-ng-gn" ,plink-ng-gn)
-        ("python-lxml" ,python-lxml) ;; used for the tests
-        ("gemma-wrapper" ,gemma-wrapper)
-        ("python-unittest" ,python-unittest2) ;; used for the tests
-        ("python-parameterized" ,python-parameterized) ;; used for the tests
-        ("genenetwork2-files-small" ,genenetwork2-files-small)
-        ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
-        ("javascript-cytoscape" ,javascript-cytoscape)
-        ("javascript-panzoom" ,javascript-cytoscape-panzoom)
-        ("javascript-qtip" ,javascript-cytoscape-qtip)
-        ("javascript-chroma" ,javascript-chroma)
-        ;; With Python3 support
-        ("gunicorn" ,gunicorn)
-        ("python-rpy2" ,python-rpy2)
-        ("python-flask" ,python-flask)
-        ("python-scipy" ,python-scipy)
-        ("python-numpy" ,python-numpy)
-        ("python-redis" ,python-redis)
-        ("python-scipy" ,python-scipy)
-        ("python-pillow" ,python-pillow)
-        ("python-reaper" ,python-reaper)
-        ("python-pyyaml" ,python-pyyaml)
-        ("python-jinja2" ,python-jinja2)
-        ("python-pandas" ,python-pandas)
-        ("python-htmlgen" ,python-htmlgen)
-        ("python-passlib" ,python-passlib)
-        ("python-wrapper" ,python-wrapper)
-        ("python-requests" ,python-requests)
-        ("python-cssselect" ,python-cssselect)
-        ("python-sqlalchemy" ,python-sqlalchemy)
-        ("python-setuptools" ,python-setuptools)
-        ("python-simplejson" ,python-simplejson)
-        ("python-xlsxwriter" ,python-xlsxwriter)
-        ("python-mysqlclient" ,python-mysqlclient)
-        ("python-elasticsearch" ,python-elasticsearch)
-        ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
-
-        ;; Without Python3 support
-        ;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program
-        ;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program
-        ;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT)
-        ;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions
-        ))
-     (build-system python-build-system)
-     (arguments
-      `(#:phases
-        (modify-phases
-          %standard-phases
-          (delete 'reset-gzip-timestamps)
-          (add-after
-            'unpack 'fix-paths-scripts
-            (lambda _
-              (substitute* "bin/genenetwork2"
-                (("/usr/bin/env") (which "env"))
-                (("python ") (string-append (which "python") " "))
-                (("readlink") (which "readlink"))
-                (("dirname") (which "dirname"))
-                (("basename") (which "basename"))
-                (("cat") (which "cat"))
-                (("echo") (which "echo"))
-                (("redis-server") (which "redis-server"))
-                (("git") (which "git"))
-                (("grep") (which "grep"))
-                (("rm") (which "rm"))
-                (("which") (which "which")))
-              #t))
-          (add-before
-            'install 'fix-paths
-            (lambda* (#:key inputs #:allow-other-keys)
-              (let* ((datafiles
-                       (string-append
-                         (assoc-ref inputs "genenetwork2-files-small")
-                         "/share/genenetwork2" ))
-                     ;; (pylmmcmd
-                     ;;  (string-append
-                     ;;   (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
-                     (plink2cmd
-                       (string-append
-                         (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
-                     (gemmacmd
-                       (string-append (assoc-ref inputs "gemma") "/bin/gemma")))
-
-                (substitute*
-                  '("etc/default_settings.py")
-                  (("^GENENETWORK_FILES +=.*")
-                   (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
-                  (("^PYLMM_COMMAND =.*")
-                   (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
-                  (("^PLINK_COMMAND =.*")
-                   (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
-                  (("^GEMMA_COMMAND =.*")
-                   (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n")))))))
-        #:tests? #f))   ; no 'setup.py test'
-     (home-page "http://genenetwork.org/")
-     (synopsis "Full genenetwork services")
-     (description "Genenetwork installation sumo.")
-     (license license:agpl3+))))
 
 (define-public genenetwork1
   (let ((commit "acf65ac9ae4be395c07c1629758f7408bf4eab5f") ; June 3, 2020